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add common names to resolver result #40
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adding parameter with_vernaculars=true will add common names information to the output |
Thanks for adding the vernacular names @dimus . Some observations:
You can find some specific example in globalbioticinteractions/globalbioticinteractions@5d6ab97 . Are these results expected? |
…eouts. hoping to discuss with @dimus see GlobalNamesArchitecture/gni#40
After running a couple of batches in production with globalbioticinteractions, I noticed that the name resolving against globalnames is causing internal server errors and gateway timeouts after the introduction of the vernacular names. I've disabled the feature for now, and hoping to re-enabled when we understand how to fix it. here's an example from the logs:
another one:
|
@dimus suggest to re-open this issue given the reported behaviors above. |
@jhpoelen -- do these examples consistently break resolver? |
yep. |
@dimus I was able to reproduce and fix the issue on my end. It turned out to be a character encoding issue in the http post request that GloBI sends to the resolver. Thanks again for adding the vernacular names to the resolver results. |
as discussed with @dimus -
In addition to taxon hierarchies, suggest to include available common names for resolved taxa. This would help me immensely in making the search features in http://globalbioticinteractions.org friendlier for humans.
Currently the resolver returns something like:
...
data_source_id: 4,
data_source_title: "NCBI",
gni_uuid: "16f235a0-e4a3-529c-9b83-bd15fe722110",
name_string: "Homo sapiens",
canonical_form: "Homo sapiens",
classification_path: "|Eukaryota|Opisthokonta|Metazoa|Eumetazoa|Bilateria|Coelomata|Deuterostomia|Chordata|Craniata|Vertebrata|Gnathostomata|Teleostomi|Euteleostomi|Sarcopterygii|Tetrapoda|Amniota|Mammalia|Theria|Eutheria|Euarchontoglires|Primates|Haplorrhini|Simiiformes|Catarrhini|Hominoidea|Hominidae|Homininae|Homo|Homo sapiens",
classification_path_ranks: "|superkingdom||kingdom|||||phylum|subphylum||superclass||||||class|||superorder|order|suborder|infraorder|parvorder|superfamily|family|subfamily|genus|species",
classification_path_ids: "131567|2759|33154|33208|6072|33213|33316|33511|7711|89593|7742|7776|117570|117571|8287|32523|32524|40674|32525|9347|314146|9443|376913|314293|9526|314295|9604|207598|9605|9606",
...
suggested result (including common names) something like:
...
data_source_id: 4,
data_source_title: "NCBI",
gni_uuid: "16f235a0-e4a3-529c-9b83-bd15fe722110",
name_string: "Homo sapiens",
canonical_form: "Homo sapiens",
common_names: "human @en|Mensch @de|mens @nl",
classification_path: "|Eukaryota|Opisthokonta|Metazoa|Eumetazoa|Bilateria|Coelomata|Deuterostomia|Chordata|Craniata|Vertebrata|Gnathostomata|Teleostomi|Euteleostomi|Sarcopterygii|Tetrapoda|Amniota|Mammalia|Theria|Eutheria|Euarchontoglires|Primates|Haplorrhini|Simiiformes|Catarrhini|Hominoidea|Hominidae|Homininae|Homo|Homo sapiens",
classification_path_ranks: "|superkingdom||kingdom|||||phylum|subphylum||superclass||||||class|||superorder|order|suborder|infraorder|parvorder|superfamily|family|subfamily|genus|species",
classification_path_ids: "131567|2759|33154|33208|6072|33213|33316|33511|7711|89593|7742|7776|117570|117571|8287|32523|32524|40674|32525|9347|314146|9443|376913|314293|9526|314295|9604|207598|9605|9606",
taxon_id: "9606",
...
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